Description

Follow-up analyses of GWIS findings

  • Table of significant and suggestive (1df GxE only) vegetable5qcm GWIS findings
  • GxE models stratified by study_design and tumor site (proximal, distal, rectal)
  • GxE models with additional covariate sets (might do this for aspirin ..)
  • Odds ratios stratified by exposure and genotype
  • Plots of model predicted outcome by 1 unit increase of exposure/allelic dosage
  • Locuszoom plot
  • Functional annotation plot

3DF

Output models stratified by sex or tumor site to check for differences in associations

chr4_91049759_C_G

Allele Freq

GxE stratified by sex

sex stratified chr4_91049759_C_G_dose x vegetable5qcm_scaled
Dependent variable:
outcome
All (Ca=29896,Co=39838) Female (Ca=14493,Co=19608) Male (Ca=15403,Co=20230)
(1) (2) (3)
chr4_91049759_C_G_dose 0.947 (0.800, 1.094) 0.853 (0.638, 1.068) 1.036 (0.834, 1.238)
vegetable5qcm_scaled 0.873*** (0.841, 0.904) 0.874*** (0.829, 0.920) 0.868*** (0.824, 0.913)
age_ref_imp 1.000 (0.998, 1.002) 1.000 (0.998, 1.003) 1.000 (0.997, 1.002)
energytot_imp 1.000*** (1.000, 1.000) 1.000*** (1.000, 1.000) 1.000*** (1.000, 1.000)
sex 0.979 (0.943, 1.015)
chr4_91049759_C_G_dose:vegetable5qcm_scaled 1.055 (0.943, 1.167) 1.101 (0.930, 1.272) 1.018 (0.869, 1.167)
Constant 0.975 (0.814, 1.135) 0.887 (0.652, 1.122) 1.025 (0.803, 1.247)
Observations 69,734 34,101 35,633
Note: p<0.05; p<0.01; p<0.001
(PC and Study estimates omitted from table)
GxE term LRtest p = 3.5059e-01
GxE term LRtest p = 2.7064e-01
GxE term LRtest p = 8.1489e-01

GxE stratified by tumor site

cancer_site_sum2 stratified chr4_91049759_C_G_dose x vegetable5qcm_scaled
Dependent variable:
outcome
All (Ca=29896,Co=39838) Proximal (Ca=9067,Co=39838) Distal (Ca=10542,Co=39838) Rectal (Ca=8432,Co=39838)
(1) (2) (3) (4)
chr4_91049759_C_G_dose 0.947 (0.800, 1.094) 0.871 (0.646, 1.096) 0.929 (0.721, 1.138) 1.119 (0.909, 1.330)
vegetable5qcm_scaled 0.873*** (0.841, 0.904) 0.874*** (0.829, 0.920) 0.884*** (0.840, 0.928) 0.860*** (0.810, 0.909)
age_ref_imp 1.000 (0.998, 1.002) 0.995*** (0.992, 0.997) 1.018*** (1.016, 1.021) 0.985*** (0.983, 0.988)
energytot_imp 1.000*** (1.000, 1.000) 1.000*** (1.000, 1.000) 1.000*** (1.000, 1.000) 1.000*** (1.000, 1.000)
sex 0.979 (0.943, 1.015) 1.018 (0.966, 1.071) 0.785*** (0.733, 0.836) 1.239*** (1.183, 1.294)
chr4_91049759_C_G_dose:vegetable5qcm_scaled 1.055 (0.943, 1.167) 1.046 (0.876, 1.215) 1.062 (0.903, 1.221) 0.948 (0.783, 1.114)
Constant 0.975 (0.814, 1.135) 0.576*** (0.353, 0.799) 0.100*** (-0.136, 0.337) 0.581*** (0.344, 0.818)
Observations 69,734 48,905 50,380 48,270
Note: p<0.05; p<0.01; p<0.001
(PC and Study estimates omitted from table)
GxE term LRtest p = 3.5059e-01
GxE term LRtest p = 6.0457e-01
GxE term LRtest p = 4.5820e-01
GxE term LRtest p = 5.2879e-01

GxE stratified by study design

study_design stratified chr4_91049759_C_G_dose x vegetable5qcm_scaled
Dependent variable:
outcome
All (Ca=29896,Co=39838) Cohort (Ca=12549,Co=24275) Case-Control (Ca=17347,Co=15563)
(1) (2) (3)
chr4_91049759_C_G_dose 0.947 (0.800, 1.094) 0.846 (0.611, 1.082) 1.018 (0.826, 1.210)
vegetable5qcm_scaled 0.873*** (0.841, 0.904) 0.936* (0.885, 0.988) 0.836*** (0.796, 0.875)
age_ref_imp 1.000 (0.998, 1.002) 1.002 (0.999, 1.005) 0.999 (0.997, 1.001)
energytot_imp 1.000*** (1.000, 1.000) 1.000 (1.000, 1.000) 1.000*** (1.000, 1.000)
sex 0.979 (0.943, 1.015) 0.993 (0.936, 1.050) 0.966 (0.920, 1.012)
chr4_91049759_C_G_dose:vegetable5qcm_scaled 1.055 (0.943, 1.167) 1.269 (0.922, 1.615) 1.008 (0.876, 1.140)
Constant 0.975 (0.814, 1.135) 3.634*** (3.180, 4.087) 1.097 (0.909, 1.285)
Observations 69,734 36,824 32,910
Note: p<0.05; p<0.01; p<0.001
(PC and Study estimates omitted from table)
GxE term LRtest p = 3.5059e-01
GxE term LRtest p = 1.7696e-01
GxE term LRtest p = 9.0934e-01

Odds Ratios

Variable is scaled by the median sex/study specific IQR, THEN centered around median / IQR (e.g. ref = median, comparison group = median + 1IQR)
G param by E
CC CG GG CG GG
vegetable5qcm_scaled=0 1 0.93 (0.8-1.08) 1.49 (0.49-4.54) 0.93 (0.8-1.08) 1.49 (0.49-4.54)
p0 P= 1 P= 0.34 P= 0.48 P= 0.34 P= 0.84
vegetable5qcm_scaled=1 0.87 (0.85-0.9) 0.86 (0.76-0.97) 1.08 (0.54-2.19) 0.99 (0.88-1.11) 1.24 (0.62-2.5)
p1 P= 1.7e-17 P= 0.017 P= 0.82 P= 0.48 P= 0.54
E param by G
vegetable5qcm_scaled 0.87 (0.85-0.9) 0.93 (0.83-1.04) 0.73 (0.31-1.7)
p P= 1.7e-17 P= 0.22 P= 0.46

Interaction Plot

Variable is scaled by the median sex/study specific IQR, THEN centered around median / IQR (e.g. ref = median, comparison group = median + 1IQR)

Locuszoom

Func Annot

Case-only

Output models stratified by sex or tumor site to check for differences in associations

chr16_70722103_G_C

Allele Freq

GxE stratified by sex

sex stratified chr16_70722103_G_C_dose x vegetable5qcm_scaled
Dependent variable:
outcome
All (Ca=29896,Co=39838) Female (Ca=14493,Co=19608) Male (Ca=15403,Co=20230)
(1) (2) (3)
chr16_70722103_G_C_dose 0.914 (0.822, 1.007) 0.879 (0.744, 1.014) 0.950 (0.822, 1.078)
vegetable5qcm_scaled 0.868*** (0.837, 0.900) 0.871*** (0.826, 0.917) 0.862*** (0.817, 0.907)
age_ref_imp 1.000 (0.998, 1.002) 1.000 (0.998, 1.003) 1.000 (0.997, 1.002)
energytot_imp 1.000*** (1.000, 1.000) 1.000*** (1.000, 1.000) 1.000*** (1.000, 1.000)
sex 0.978 (0.942, 1.014)
chr16_70722103_G_C_dose:vegetable5qcm_scaled 1.112** (1.035, 1.189) 1.120 (1.002, 1.239) 1.102 (1.000, 1.204)
Constant 0.977 (0.816, 1.137) 0.889 (0.654, 1.124) 1.027 (0.805, 1.249)
Observations 69,734 34,101 35,633
Note: p<0.05; p<0.01; p<0.001
(PC and Study estimates omitted from table)
GxE term LRtest p = 6.9667e-03
GxE term LRtest p = 5.9571e-02
GxE term LRtest p = 6.2158e-02

GxE stratified by tumor site

cancer_site_sum2 stratified chr16_70722103_G_C_dose x vegetable5qcm_scaled
Dependent variable:
outcome
All (Ca=29896,Co=39838) Proximal (Ca=9067,Co=39838) Distal (Ca=10542,Co=39838) Rectal (Ca=8432,Co=39838)
(1) (2) (3) (4)
chr16_70722103_G_C_dose 0.914 (0.822, 1.007) 0.766*** (0.616, 0.916) 0.937 (0.803, 1.071) 1.023 (0.883, 1.164)
vegetable5qcm_scaled 0.868*** (0.837, 0.900) 0.868*** (0.822, 0.913) 0.878*** (0.834, 0.922) 0.853*** (0.803, 0.903)
age_ref_imp 1.000 (0.998, 1.002) 0.995*** (0.993, 0.998) 1.018*** (1.016, 1.021) 0.985*** (0.983, 0.988)
energytot_imp 1.000*** (1.000, 1.000) 1.000*** (1.000, 1.000) 1.000*** (1.000, 1.000) 1.000*** (1.000, 1.000)
sex 0.978 (0.942, 1.014) 1.017 (0.965, 1.070) 0.784*** (0.733, 0.836) 1.237*** (1.182, 1.293)
chr16_70722103_G_C_dose:vegetable5qcm_scaled 1.112** (1.035, 1.189) 1.168* (1.049, 1.286) 1.143* (1.033, 1.252) 1.078 (0.963, 1.193)
Constant 0.977 (0.816, 1.137) 0.577*** (0.354, 0.800) 0.101*** (-0.136, 0.337) 0.582*** (0.345, 0.819)
Observations 69,734 48,905 50,380 48,270
Note: p<0.05; p<0.01; p<0.001
(PC and Study estimates omitted from table)
GxE term LRtest p = 6.9667e-03
GxE term LRtest p = 1.0792e-02
GxE term LRtest p = 1.7406e-02
GxE term LRtest p = 2.0394e-01

GxE stratified by study design

study_design stratified chr16_70722103_G_C_dose x vegetable5qcm_scaled
Dependent variable:
outcome
All (Ca=29896,Co=39838) Cohort (Ca=12549,Co=24275) Case-Control (Ca=17347,Co=15563)
(1) (2) (3)
chr16_70722103_G_C_dose 0.914 (0.822, 1.007) 0.944 (0.814, 1.073) 0.876 (0.742, 1.011)
vegetable5qcm_scaled 0.868*** (0.837, 0.900) 0.936* (0.884, 0.987) 0.827*** (0.787, 0.867)
age_ref_imp 1.000 (0.998, 1.002) 1.002 (0.999, 1.006) 0.999 (0.997, 1.001)
energytot_imp 1.000*** (1.000, 1.000) 1.000 (1.000, 1.000) 1.000*** (1.000, 1.000)
sex 0.978 (0.942, 1.014) 0.993 (0.936, 1.049) 0.965 (0.919, 1.011)
chr16_70722103_G_C_dose:vegetable5qcm_scaled 1.112** (1.035, 1.189) 1.102 (0.928, 1.277) 1.138** (1.042, 1.233)
Constant 0.977 (0.816, 1.137) 3.635*** (3.181, 4.088) 1.102 (0.914, 1.290)
Observations 69,734 36,824 32,910
Note: p<0.05; p<0.01; p<0.001
(PC and Study estimates omitted from table)
GxE term LRtest p = 6.9667e-03
GxE term LRtest p = 2.7212e-01
GxE term LRtest p = 7.8922e-03

Odds Ratios

Variable is scaled by the median sex/study specific IQR, THEN centered around median / IQR (e.g. ref = median, comparison group = median + 1IQR)
G param by E
GG GC CC GC CC
vegetable5qcm_scaled=0 1 0.92 (0.83-1.01) 0.78 (0.32-1.91) 0.92 (0.83-1.01) 0.78 (0.32-1.91)
p0 P= 1 P= 0.072 P= 0.59 P= 0.072 P= 0.55
vegetable5qcm_scaled=1 0.87 (0.84-0.9) 0.89 (0.81-0.98) 0.73 (0.39-1.38) 1.03 (0.94-1.12) 0.84 (0.44-1.59)
p1 P= 1.3e-18 P= 0.013 P= 0.33 P= 0.59 P= 0.59
E param by G
vegetable5qcm_scaled 0.87 (0.84-0.9) 0.97 (0.9-1.06) 0.93 (0.52-1.69)
p P= 1.3e-18 P= 0.51 P= 0.82

Interaction Plot

Variable is scaled by the median sex/study specific IQR, THEN centered around median / IQR (e.g. ref = median, comparison group = median + 1IQR)

Locuszoom

Func Annot

Two-step (excluding GWAS loci)

chr5_112341879_T_C

Allele Freq

GxE stratified by sex

sex stratified chr5_112341879_T_C_dose x vegetable5qcm_scaled
Dependent variable:
outcome
All (Ca=29896,Co=39838) Female (Ca=14493,Co=19608) Male (Ca=15403,Co=20230)
(1) (2) (3)
chr5_112341879_T_C_dose 1.177** (1.076, 1.279) 1.025 (0.877, 1.173) 1.328*** (1.189, 1.467)
vegetable5qcm_scaled 0.869*** (0.837, 0.900) 0.869*** (0.823, 0.914) 0.864*** (0.820, 0.909)
age_ref_imp 1.000 (0.998, 1.002) 1.000 (0.998, 1.003) 1.000 (0.997, 1.002)
energytot_imp 1.000*** (1.000, 1.000) 1.000*** (1.000, 1.000) 1.000*** (1.000, 1.000)
sex 0.979 (0.943, 1.015)
chr5_112341879_T_C_dose:vegetable5qcm_scaled 1.145** (1.054, 1.235) 1.228** (1.094, 1.361) 1.088 (0.965, 1.211)
Constant 0.969 (0.808, 1.130) 0.883 (0.648, 1.118) 1.019 (0.797, 1.242)
Observations 69,734 34,101 35,633
Note: p<0.05; p<0.01; p<0.001
(PC and Study estimates omitted from table)
GxE term LRtest p = 3.0645e-03
GxE term LRtest p = 2.2313e-03
GxE term LRtest p = 1.7725e-01

GxE stratified by tumor site

cancer_site_sum2 stratified chr5_112341879_T_C_dose x vegetable5qcm_scaled
Dependent variable:
outcome
All (Ca=29896,Co=39838) Proximal (Ca=9067,Co=39838) Distal (Ca=10542,Co=39838) Rectal (Ca=8432,Co=39838)
(1) (2) (3) (4)
chr5_112341879_T_C_dose 1.177** (1.076, 1.279) 1.161 (1.011, 1.310) 1.130 (0.985, 1.274) 1.231** (1.080, 1.383)
vegetable5qcm_scaled 0.869*** (0.837, 0.900) 0.865*** (0.819, 0.911) 0.884*** (0.841, 0.928) 0.849*** (0.799, 0.899)
age_ref_imp 1.000 (0.998, 1.002) 0.995*** (0.993, 0.998) 1.018*** (1.016, 1.021) 0.985*** (0.983, 0.988)
energytot_imp 1.000*** (1.000, 1.000) 1.000*** (1.000, 1.000) 1.000*** (1.000, 1.000) 1.000*** (1.000, 1.000)
sex 0.979 (0.943, 1.015) 1.019 (0.966, 1.072) 0.785*** (0.734, 0.837) 1.240*** (1.184, 1.295)
chr5_112341879_T_C_dose:vegetable5qcm_scaled 1.145** (1.054, 1.235) 1.249*** (1.123, 1.374) 1.042 (0.909, 1.176) 1.191** (1.062, 1.320)
Constant 0.969 (0.808, 1.130) 0.570*** (0.347, 0.793) 0.100*** (-0.137, 0.336) 0.578*** (0.341, 0.815)
Observations 69,734 48,905 50,380 48,270
Note: p<0.05; p<0.01; p<0.001
(PC and Study estimates omitted from table)
GxE term LRtest p = 3.0645e-03
GxE term LRtest p = 5.2089e-04
GxE term LRtest p = 5.4377e-01
GxE term LRtest p = 8.2200e-03

GxE stratified by study design

study_design stratified chr5_112341879_T_C_dose x vegetable5qcm_scaled
Dependent variable:
outcome
All (Ca=29896,Co=39838) Cohort (Ca=12549,Co=24275) Case-Control (Ca=17347,Co=15563)
(1) (2) (3)
chr5_112341879_T_C_dose 1.177** (1.076, 1.279) 1.166* (1.024, 1.308) 1.166* (1.020, 1.311)
vegetable5qcm_scaled 0.869*** (0.837, 0.900) 0.938* (0.886, 0.989) 0.828*** (0.788, 0.868)
age_ref_imp 1.000 (0.998, 1.002) 1.002 (0.999, 1.006) 0.999 (0.997, 1.001)
energytot_imp 1.000*** (1.000, 1.000) 1.000 (1.000, 1.000) 1.000*** (1.000, 1.000)
sex 0.979 (0.943, 1.015) 0.993 (0.936, 1.050) 0.966 (0.920, 1.012)
chr5_112341879_T_C_dose:vegetable5qcm_scaled 1.145** (1.054, 1.235) 1.041 (0.841, 1.242) 1.173** (1.062, 1.283)
Constant 0.969 (0.808, 1.130) 3.603*** (3.149, 4.056) 1.093 (0.905, 1.282)
Observations 69,734 36,824 32,910
Note: p<0.05; p<0.01; p<0.001
(PC and Study estimates omitted from table)
GxE term LRtest p = 3.0645e-03
GxE term LRtest p = 6.9294e-01
GxE term LRtest p = 4.4907e-03

Odds Ratios

Variable is scaled by the median sex/study specific IQR, THEN centered around median / IQR (e.g. ref = median, comparison group = median + 1IQR)
G param by E
TT TC CC TC CC
vegetable5qcm_scaled=0 1 1.19 (1.08-1.33) 0.86 (0.36-2.06) 1.19 (1.08-1.33) 0.86 (0.36-2.06)
p0 P= 1 P= 0.00085 P= 0.73 P= 0.00085 P= 4.1e-09
vegetable5qcm_scaled=1 0.87 (0.84-0.9) 1.17 (1.06-1.3) 1.4 (0.67-2.92) 1.35 (1.22-1.5) 1.61 (0.78-3.36)
p1 P= 1.6e-18 P= 0.0023 P= 0.37 P= 0.73 P= 0.2
E param by G
vegetable5qcm_scaled 0.87 (0.84-0.9) 0.98 (0.9-1.08) 1.63 (0.76-3.52)
p P= 1.6e-18 P= 0.74 P= 0.21

Interaction Plot

Variable is scaled by the median sex/study specific IQR, THEN centered around median / IQR (e.g. ref = median, comparison group = median + 1IQR)

Locuszoom

Func Annot

chr5_112500404_T_C

Allele Freq

GxE stratified by sex

sex stratified chr5_112500404_T_C_dose x vegetable5qcm_scaled
Dependent variable:
outcome
All (Ca=29896,Co=39838) Female (Ca=14493,Co=19608) Male (Ca=15403,Co=20230)
(1) (2) (3)
chr5_112500404_T_C_dose 1.166* (1.030, 1.302) 1.131 (0.935, 1.327) 1.188 (0.999, 1.377)
vegetable5qcm_scaled 0.869*** (0.838, 0.900) 0.870*** (0.825, 0.916) 0.865*** (0.821, 0.909)
age_ref_imp 1.000 (0.998, 1.002) 1.001 (0.998, 1.003) 1.000 (0.997, 1.002)
energytot_imp 1.000*** (1.000, 1.000) 1.000*** (1.000, 1.000) 1.000*** (1.000, 1.000)
sex 0.979 (0.943, 1.015)
chr5_112500404_T_C_dose:vegetable5qcm_scaled 1.199** (1.090, 1.307) 1.301** (1.137, 1.466) 1.123 (0.978, 1.269)
Constant 0.974 (0.813, 1.135) 0.882 (0.647, 1.117) 1.030 (0.807, 1.252)
Observations 69,734 34,101 35,633
Note: p<0.05; p<0.01; p<0.001
(PC and Study estimates omitted from table)
GxE term LRtest p = 9.6238e-04
GxE term LRtest p = 1.3470e-03
GxE term LRtest p = 1.1535e-01

GxE stratified by tumor site

cancer_site_sum2 stratified chr5_112500404_T_C_dose x vegetable5qcm_scaled
Dependent variable:
outcome
All (Ca=29896,Co=39838) Proximal (Ca=9067,Co=39838) Distal (Ca=10542,Co=39838) Rectal (Ca=8432,Co=39838)
(1) (2) (3) (4)
chr5_112500404_T_C_dose 1.166* (1.030, 1.302) 1.229* (1.034, 1.425) 1.047 (0.848, 1.247) 1.314** (1.116, 1.512)
vegetable5qcm_scaled 0.869*** (0.838, 0.900) 0.870*** (0.824, 0.915) 0.882*** (0.838, 0.926) 0.852*** (0.802, 0.901)
age_ref_imp 1.000 (0.998, 1.002) 0.995*** (0.993, 0.998) 1.018*** (1.016, 1.021) 0.985*** (0.983, 0.988)
energytot_imp 1.000*** (1.000, 1.000) 1.000*** (1.000, 1.000) 1.000*** (1.000, 1.000) 1.000*** (1.000, 1.000)
sex 0.979 (0.943, 1.015) 1.018 (0.965, 1.071) 0.785*** (0.733, 0.836) 1.239*** (1.184, 1.294)
chr5_112500404_T_C_dose:vegetable5qcm_scaled 1.199** (1.090, 1.307) 1.220** (1.070, 1.370) 1.153 (0.995, 1.312) 1.199* (1.048, 1.349)
Constant 0.974 (0.813, 1.135) 0.572*** (0.349, 0.795) 0.100*** (-0.136, 0.337) 0.581*** (0.344, 0.818)
Observations 69,734 48,905 50,380 48,270
Note: p<0.05; p<0.01; p<0.001
(PC and Study estimates omitted from table)
GxE term LRtest p = 9.6238e-04
GxE term LRtest p = 9.3777e-03
GxE term LRtest p = 7.9311e-02
GxE term LRtest p = 1.8479e-02

GxE stratified by study design

study_design stratified chr5_112500404_T_C_dose x vegetable5qcm_scaled
Dependent variable:
outcome
All (Ca=29896,Co=39838) Cohort (Ca=12549,Co=24275) Case-Control (Ca=17347,Co=15563)
(1) (2) (3)
chr5_112500404_T_C_dose 1.166* (1.030, 1.302) 1.209 (1.012, 1.406) 1.153 (0.959, 1.347)
vegetable5qcm_scaled 0.869*** (0.838, 0.900) 0.934** (0.882, 0.985) 0.830*** (0.790, 0.869)
age_ref_imp 1.000 (0.998, 1.002) 1.002 (0.999, 1.006) 0.999 (0.997, 1.001)
energytot_imp 1.000*** (1.000, 1.000) 1.000 (1.000, 1.000) 1.000*** (1.000, 1.000)
sex 0.979 (0.943, 1.015) 0.994 (0.937, 1.050) 0.966 (0.919, 1.012)
chr5_112500404_T_C_dose:vegetable5qcm_scaled 1.199** (1.090, 1.307) 1.506** (1.219, 1.794) 1.177* (1.044, 1.310)
Constant 0.974 (0.813, 1.135) 3.589*** (3.136, 4.043) 1.099 (0.910, 1.287)
Observations 69,734 36,824 32,910
Note: p<0.05; p<0.01; p<0.001
(PC and Study estimates omitted from table)
GxE term LRtest p = 9.6238e-04
GxE term LRtest p = 4.3001e-03
GxE term LRtest p = 1.6174e-02

Odds Ratios

Variable is scaled by the median sex/study specific IQR, THEN centered around median / IQR (e.g. ref = median, comparison group = median + 1IQR)
G param by E
TT TC CC TC CC
vegetable5qcm_scaled=0 1 1.17 (1.02-1.35) 0.82 (0.17-3.92) 1.17 (1.02-1.35) 0.82 (0.17-3.92)
p0 P= 1 P= 0.024 P= 0.81 P= 0.024 P= 6.1e-08
vegetable5qcm_scaled=1 0.87 (0.84-0.9) 1.21 (1.07-1.36) 1.79 (0.67-4.83) 1.39 (1.23-1.56) 2.06 (0.77-5.55)
p1 P= 1.9e-18 P= 0.0025 P= 0.25 P= 0.81 P= 0.15
E param by G
vegetable5qcm_scaled 0.87 (0.84-0.9) 1.03 (0.92-1.15) 2.18 (0.65-7.34)
p P= 1.9e-18 P= 0.61 P= 0.21

Interaction Plot

Variable is scaled by the median sex/study specific IQR, THEN centered around median / IQR (e.g. ref = median, comparison group = median + 1IQR)

Locuszoom

Func Annot

chr5_114126148_G_A

Allele Freq

GxE stratified by sex

sex stratified chr5_114126148_G_A_dose x vegetable5qcm_scaled
Dependent variable:
outcome
All (Ca=29896,Co=39838) Female (Ca=14493,Co=19608) Male (Ca=15403,Co=20230)
(1) (2) (3)
chr5_114126148_G_A_dose 1.103 (0.987, 1.219) 1.156 (0.987, 1.325) 1.060 (0.901, 1.219)
vegetable5qcm_scaled 0.867*** (0.836, 0.899) 0.873*** (0.827, 0.918) 0.860*** (0.815, 0.904)
age_ref_imp 1.000 (0.998, 1.002) 1.000 (0.998, 1.003) 1.000 (0.997, 1.002)
energytot_imp 1.000*** (1.000, 1.000) 1.000*** (1.000, 1.000) 1.000*** (1.000, 1.000)
sex 0.978 (0.942, 1.014)
chr5_114126148_G_A_dose:vegetable5qcm_scaled 1.197*** (1.099, 1.295) 1.150 (1.002, 1.298) 1.234** (1.104, 1.365)
Constant 0.976 (0.816, 1.137) 0.886 (0.651, 1.121) 1.028 (0.806, 1.251)
Observations 69,734 34,101 35,633
Note: p<0.05; p<0.01; p<0.001
(PC and Study estimates omitted from table)
GxE term LRtest p = 2.6701e-04
GxE term LRtest p = 6.1220e-02
GxE term LRtest p = 1.3906e-03

GxE stratified by tumor site

cancer_site_sum2 stratified chr5_114126148_G_A_dose x vegetable5qcm_scaled
Dependent variable:
outcome
All (Ca=29896,Co=39838) Proximal (Ca=9067,Co=39838) Distal (Ca=10542,Co=39838) Rectal (Ca=8432,Co=39838)
(1) (2) (3) (4)
chr5_114126148_G_A_dose 1.103 (0.987, 1.219) 1.117 (0.945, 1.289) 1.096 (0.931, 1.261) 1.247* (1.076, 1.419)
vegetable5qcm_scaled 0.867*** (0.836, 0.899) 0.867*** (0.821, 0.913) 0.884*** (0.840, 0.928) 0.851*** (0.802, 0.901)
age_ref_imp 1.000 (0.998, 1.002) 0.995*** (0.992, 0.997) 1.018*** (1.016, 1.021) 0.985*** (0.983, 0.988)
energytot_imp 1.000*** (1.000, 1.000) 1.000*** (1.000, 1.000) 1.000*** (1.000, 1.000) 1.000*** (1.000, 1.000)
sex 0.978 (0.942, 1.014) 1.017 (0.965, 1.070) 0.785*** (0.733, 0.836) 1.238*** (1.183, 1.293)
chr5_114126148_G_A_dose:vegetable5qcm_scaled 1.197*** (1.099, 1.295) 1.244** (1.107, 1.381) 1.047 (0.903, 1.192) 1.170* (1.029, 1.311)
Constant 0.976 (0.816, 1.137) 0.576*** (0.353, 0.798) 0.100*** (-0.136, 0.337) 0.583*** (0.346, 0.820)
Observations 69,734 48,905 50,380 48,270
Note: p<0.05; p<0.01; p<0.001
(PC and Study estimates omitted from table)
GxE term LRtest p = 2.6701e-04
GxE term LRtest p = 1.7517e-03
GxE term LRtest p = 5.3167e-01
GxE term LRtest p = 2.9371e-02

GxE stratified by study design

study_design stratified chr5_114126148_G_A_dose x vegetable5qcm_scaled
Dependent variable:
outcome
All (Ca=29896,Co=39838) Cohort (Ca=12549,Co=24275) Case-Control (Ca=17347,Co=15563)
(1) (2) (3)
chr5_114126148_G_A_dose 1.103 (0.987, 1.219) 1.009 (0.845, 1.172) 1.219* (1.049, 1.389)
vegetable5qcm_scaled 0.867*** (0.836, 0.899) 0.931** (0.879, 0.982) 0.831*** (0.791, 0.870)
age_ref_imp 1.000 (0.998, 1.002) 1.002 (0.999, 1.006) 0.999 (0.997, 1.001)
energytot_imp 1.000*** (1.000, 1.000) 1.000 (1.000, 1.000) 1.000*** (1.000, 1.000)
sex 0.978 (0.942, 1.014) 0.993 (0.936, 1.050) 0.965 (0.919, 1.012)
chr5_114126148_G_A_dose:vegetable5qcm_scaled 1.197*** (1.099, 1.295) 1.445** (1.209, 1.682) 1.118 (0.998, 1.238)
Constant 0.976 (0.816, 1.137) 3.600*** (3.146, 4.053) 1.100 (0.912, 1.289)
Observations 69,734 36,824 32,910
Note: p<0.05; p<0.01; p<0.001
(PC and Study estimates omitted from table)
GxE term LRtest p = 2.6701e-04
GxE term LRtest p = 2.0503e-03
GxE term LRtest p = 6.7241e-02

Odds Ratios

Variable is scaled by the median sex/study specific IQR, THEN centered around median / IQR (e.g. ref = median, comparison group = median + 1IQR)
G param by E
GG GA AA GA AA
vegetable5qcm_scaled=0 1 1.1 (0.97-1.24) 1.47 (0.45-4.78) 1.1 (0.97-1.24) 1.47 (0.45-4.78)
p0 P= 1 P= 0.12 P= 0.52 P= 0.12 P= 2.3e-06
vegetable5qcm_scaled=1 0.87 (0.84-0.9) 1.12 (1.01-1.25) 2.94 (1.07-8.13) 1.29 (1.16-1.44) 3.39 (1.23-9.36)
p1 P= 8.4e-19 P= 0.038 P= 0.037 P= 0.52 P= 0.018
E param by G
vegetable5qcm_scaled 0.87 (0.84-0.9) 1.02 (0.93-1.13) 2 (0.72-5.54)
p P= 8.4e-19 P= 0.65 P= 0.18

Interaction Plot

Variable is scaled by the median sex/study specific IQR, THEN centered around median / IQR (e.g. ref = median, comparison group = median + 1IQR)

Locuszoom

Func Annot